I used the exact NES palette for this. It's indeed 8bit in everything. If you notice I also respected the spritemap requirements for an NES game. If Binding of Isaac was to be released for NES, this is how it would probably look like.
I hate to admit it, but you are right. The shader needs more blur and I need to find a way to make the pixels non square. Well we can still pretend that this is a newer Sony Trinitron CRT TV (if it wasn't flat), right? For the colours I used the original limited NES palette and then applied the NTSC filter to be as precise to the real thing as possible, so I didn't have much choice on the matter.